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GenomiPhi amplification of FFPE tissue DNA for array CGH

Key words: formalin-fixed paraffin-embedded (FFPE) • GenomiPhi • whole-genome amplification (WGA) • degenerate oligonucleotideprimed PCR (DOP-PCR) • Cy3/Cy5-dCTP probe labeling • comparative genomic hybridization (CGH) • bacterial artificial chromosome (BAC) array • array CGH


Human genomic DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissue samples was amplified using the GenomiPhi™ DNA Amplification Kit, fluorescently labeled with Cy™3 and Cy5 dyes, and hybridized to human BAC microarrays. Commercially available human BAC arrays from Spectral Genomics were chosen to verify the methods. Array data quality was similar to that obtained using the DOP-PCR method, demonstrating the application of GenomiPhi DNA Amplification Kit in array CGH experiments.


Introduction
Formalin-fixed paraffin-embedded (FFPE) tissues have been widely used to archive samples obtained from biopsies of various human cancers and diseased tissues linked to genetic abnormalities. The characterization of FFPE samples by clinical laboratories is mostly limited to cytogenetic techniques that analyze genetic changes at the chromosomal level (1). Because DNA purified from FFPE tissue slides is highly degraded, damaged, and available only in small quantities, there has been little molecular analysis of these samples. Extracting molecular information on genome integrity and DNA copy-number changes from FFPE samples has the potential to drastically improve our understanding of genetic disorders underlying disease states.

With the emergence of comparative genomic hybridization (CGH) using microarrays spotted with cloned DNA sequences, such as bacterial artificial chromosome (BAC) arrays, it has become possible to obtain whole-genome information on allelic differences between samples from normal vs d
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